Project Summary Broad long-term objectives: In Specific Aim 1, we will determine the phenotypes (e.g. 7 mitochondrially targeted drugs; non-mitochondrially targeted drugs; growth at low and high temperature) of 98 L-A strain pairs. We will identify strain pairs with strong L-A-dependent phenotypes; that is, N1/N1 ?1 L-A0 ? N1/N1 ?1 L-A+. We will also identify candidate QTGs for analysis in Aim 3. In Specific Aim 2, we will determine the phenotypes (e.g. 7 mitochondrially targeted drugs; non-mitochondrially targeted drugs; growth at low and high temperature) of iso- nuclear pairs of F1; for example, N1 ?1 ? N2 ?0 ? N1/N2 ?1 and N1 ?0 ? N2 ?2 ? N1/N2 ?2. We will identify iso-nuclear F1 diploid strain pairs with strong mitochondrial genome-dependent phenotypes; that is, N1/N2 ?1 ? N1/N2 ?2. We will cross strains with strong mitochondrial genome-dependent phenotypes; for example, N1 ?1 ? N2 ?2 ? F1 N1/N2 (? recombinants). In multiple F1 N1/N2 (? recombinants) diploids, we will identify phenotypically relevant mitochondrial (?) QTG(s). In Specific Aim 3A, using our results from Aim 1 and 2, we will perform RNA-Seq on ethanol and dextrose grown isogenic L-A parent strains and L-A- and ? genotype-controlled iso-nuclear F1. We will identify L-A and ? genotype-dependent effects on the transcriptomes and potential candidate QTGs, which will aid downstream analysis. In Specific Aim 3B, we will (separately) sporulate multiple iso-nuclear F1 strain pairs with strong L-A- and/or mitochondrial genome-dependent phenotypes (identified in Aim 1, 2; RNA-Seq in Aim 3B) to generate L-A- and ? genotype-controlled F12 populations. In multiple L-A F12 ?1 vs. L-A F12 ?2 population pairs, we will identify phenotypically relevant nuclear QTGs. We will primarily focus on L-A and ? genotype-specific nuclear QTGs to advance our understanding of missing heritability, host-virus, and N-? interactions.